Being hit by lightning, burned alive, falling on jagged rocks, getting impaled, receiving multiple gunshot wounds, and finally being mauled and split into pieces by a mountain lion AND a grizzly bear, only to later be brought to life as Darth Chef

I think you missed the overall point. Did you even listen to Kyle's(I believe it was Kyle, anyway...) closing monologue? He said that they ultimately should not and do not hate Chef(Hayes), but they hate the "stupid club" he was in.

Sure, they're pissed off and angry about the situation...but they're obviously blaming Scientology more than Hayes himself for this situation. It's not entirely his fault; it's a controlling and manipulative pseudo-religion that essentially brainwashes it's members into marching lockstep. They didn't like what South Park had said, so they probably told him to quit. And he did.

I think they gave the character a proper sendoff...and besides, now they have a possible "villain character" to use from time to time. Darth Chef can always occasionally pop in for some comedic evil.